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- PDB-6qjt: Thermophage P23-45 in situ procapsid portal protein -

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Entry
Database: PDB / ID: 6qjt
TitleThermophage P23-45 in situ procapsid portal protein
ComponentsPortal protein
KeywordsVIRAL PROTEIN / portal / translocase / motor / pore / bacteriophage / thermophage / caudovirales / siphoviridae / virus
Function / homologyviral capsid / Portal protein
Function and homology information
Biological speciesThermus virus P23-45
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsBayfield, O.W. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust206377 United Kingdom
Wellcome Trust103460 United Kingdom
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structure in situ reveals a molecular switch that safeguards virus against genome loss.
Authors: Oliver W Bayfield / Alasdair C Steven / Alfred A Antson /
Abstract: The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is ...The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid, and how these processes are controlled. A cryo-EM structure of the portal protein of thermostable virus P23-45, determined in situ in its procapsid-bound state, indicates a mechanism that naturally safeguards the virus against genome loss. This occurs via an inversion of the conformation of the loops that define the constriction in the central tunnel, accompanied by a hydrophilic-hydrophobic switch. The structure also shows how translocation of DNA into the capsid could be modulated by a changing mode of protein-protein interactions between portal and capsid, across a symmetry-mismatched interface.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 3, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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Assembly

Deposited unit
A: Portal protein


Theoretical massNumber of molelcules
Total (without water)49,7141
Polymers49,7141
Non-polymers00
Water0
1
A: Portal protein
x 12


Theoretical massNumber of molelcules
Total (without water)596,57012
Polymers596,57012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11

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Components

#1: Protein Portal protein


Mass: 49714.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus virus P23-45 / Cell line: Thermus thermophilus HB8 / References: UniProt: A7XXB9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Thermus phage P2345 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.596 MDa / Experimental value: YES
Source (natural)Organism: Thermus phage P2345 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Thermus thermophilus HB8
Virus shellTriangulation number (T number): 7
Buffer solutionpH: 8
Buffer component
IDConc.FormulaBuffer-ID
1100 mMNaClSodium chloride1
220 mMTris-HClTris1
310 mMMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 99 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
2Scipionparticle selection
3EPUimage acquisition
5CTFFINDCTF correction
8Cootmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
14PHENIXmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10025 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 3.74 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053276
ELECTRON MICROSCOPYf_angle_d0.8424450
ELECTRON MICROSCOPYf_dihedral_angle_d11.7081964
ELECTRON MICROSCOPYf_chiral_restr0.051505
ELECTRON MICROSCOPYf_plane_restr0.007574

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